Question

You digest a plasmid with a restriction enzyme that recognizes a single site on the plasmid. When you perform gel electrophoresis on the digestion product, you quickly realize that there are two bands; one at the expected size and one near the well. Which of the following best explains the outcome?

a.DNA was trapped in the agarose gel
b.Some plasmids were not digested
c.The presence of the chromosomal DNA
d.The some plasmids ligated together

Answer 1

When the solution containing plasmid DNA was digested with a restriction enzyme, which recognize at single site on the plasmid, produce single band with additional band near the loading well suggest following possibilities

1. the plasmid DNA solution is a mixture of plasmid DNA and genomic DNA, which is not digested by restriction enzyme.  

2. the plasmid DNA solution is a mixture of plasmid DNA and mitochondrial or chloroplast circular DNA, which is not digested by restriction enzyme.

3. the restricted or digested plasmid DNA solution is a mixture of digested and undigested plasmid DNA.

4. some of the DNA is trapped near the well due to exceptionally large size of DNA.

So, as per the options given in the questions

option b. and c. seems to be correct

a. is not correct because plasmid or chromosomal DNA is never trapped

d. is not correct because plasmid cannot ligate by restriction enzymes.